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- PDB-6iy4: Crystal structure of a psychrophilic marine protease MP inhibitor -

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Basic information

Entry
Database: PDB / ID: 6iy4
TitleCrystal structure of a psychrophilic marine protease MP inhibitor
ComponentsLupI
KeywordsHYDROLASE INHIBITOR / psychrophilic marine protease inhibitor
Function / homologyProtease inhibitor / Alkaline proteinase inhibitor/ Outer membrane lipoprotein Omp19 / Protease inhibitor Inh / Protease inhibitor, beta-barrel domain / metalloendopeptidase inhibitor activity / periplasmic space / LupI
Function and homology information
Biological speciesFlavobacterium sp. YS-80-122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsHao, J.H. / Zhang, L.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China41376175 China
CitationJournal: To be published
Title: Crystal structure of a psychrophilic marine protease MP inhibitor
Authors: Hao, J.H.
History
DepositionDec 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: LupI


Theoretical massNumber of molelcules
Total (without water)10,1041
Polymers10,1041
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5110 Å2
Unit cell
Length a, b, c (Å)34.036, 39.281, 62.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LupI


Mass: 10104.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium sp. YS-80-122 (bacteria) / Plasmid details: yellow sea in china / References: UniProt: G3MEU6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAuthor states that the sequence G3MEU6 may have errors in sequencing, and this time the sequence is ...Author states that the sequence G3MEU6 may have errors in sequencing, and this time the sequence is re-sequence verified to be Leu.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5 / Details: 0.1M NaCl, 0.1M BIS-TRIS pH 6.5, 1.5M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 11707 / % possible obs: 99.7 % / Redundancy: 5.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.088 / Net I/σ(I): 11
Reflection shellResolution: 1.59→1.64 Å / Rmerge(I) obs: 0.654 / Num. unique obs: 5628 / CC1/2: 0.869 / Rpim(I) all: 0.277

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IXX

6ixx


Resolution: 1.59→31.31 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.784 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.09
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 569 4.9 %RANDOM
Rwork0.2098 ---
obs0.2102 11159 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 67.91 Å2 / Biso mean: 25.274 Å2 / Biso min: 16.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0 Å2
2---1.22 Å20 Å2
3---1.32 Å2
Refinement stepCycle: final / Resolution: 1.59→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms709 0 0 13 722
Biso mean---27.4 -
Num. residues----93
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013724
X-RAY DIFFRACTIONr_bond_other_d0.0010.017668
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.645983
X-RAY DIFFRACTIONr_angle_other_deg1.4751.5751550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.778592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16421.76534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41315120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.809155
X-RAY DIFFRACTIONr_chiral_restr0.0710.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02809
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02154
LS refinement shellResolution: 1.586→1.627 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 35 -
Rwork0.23 710 -
all-745 -
obs--84.85 %

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